nf-core/samtools/bam2fq @ 0.0.0-6c4ed3a
Summary
The module uses bam2fq method from samtools to convert a SAM, BAM or CRAM file to FASTQ format
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_BAM2FQ } from 'nf-core/samtools/bam2fq'
License
MIT License
Name
|
SAMTOOLS_BAM2FQ |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
inputbam
file
|
BAM/CRAM/SAM file *.{bam,cram,sam}
|
split
boolean
|
TRUE/FALSE value to indicate if reads should be separated into /1, /2 and if present other, or singleton. Note: choosing TRUE will generate 4 different files. Choosing FALSE will produce a single file, which will be interleaved in case the input contains paired reads. |
|---|
reads
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.fq.gz
file
|
FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) or a single interleaved .fq.gz file if the user chooses not to split the reads. *.fq.gz
|
versions_samtools
tuple
${task.process}
string
|
The name of the process |
|---|---|
samtools
string
|
The name of the tool |
samtools version | sed '1!d;s/.* //'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samtools | Tools for dealing with SAM, BAM and CRAM files | n/a |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:42:03 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Fbam2fq/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/bam2fq/blobs/sha256:d220db7d2c9ad4af6c4a38ec290bcabf52d23b044686086816721d84d92efceb |
| Size | 3.1 KB |
| Checksum | sha256:d220db7d2c9ad4af6c4a38ec290bcabf52d23b044686086816721d84d92efceb |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:42:03 (UTC) | 3 | 3.1 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:33:17 (UTC) | 3 | 3.0 KB |